A python package for circDraw visualization
Project description
circDraw
A python package for circDraw visualization
Usage
from circDraw import circDraw
# initiate a circDraw instance
cd = circDraw()
# set color of circ_on_chr (optional)
cd.set_palette(["#5CA0F2", "#FF881D", '#e30067', '#924900','#ab9c00','#ccd0d2', '#075800', '#5e0094',])
# set color of modifications (optional)
mod_palette = {'m6a': '#E98B2A',
'm5c': '#E16B8C',
'm1a': '#64363C',
'pu': '#ffa12c',
'2ome': '#1a6f00',
'mre': '#6D2E5B',
'rbp': "#2B5F75",
'orf': '#516E41'}
cd.set_mod_palette(mod_palette)
# draw backsplicing site on chromosome region
cd.circ_on_chr('Your file')
# draw modifications on circRNA
cd.mod_on_circ('Your file')
API
#####circ_on_chr
circDraw.circ_on_chr(file, title='circDraw', dpi=300, save='png', show=True, size=(10, 5))
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File:
-
Only supported 'csv'
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Start End Type Name Color (Optional) -
Start < End
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Type: circ, exon, intron, gene
-
Color: RGB, RGBA, hex, or supported color names.
-
-
Title: The title of the plot
-
Save: file format you wish to save as, PNG, PDF, JPEG, etc.
-
Show: Bool, wheather to show the plot after rendering.
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Size: (Length, Width) the size of the plot.
#####mod_on_circ
circDraw.mod_on_circ(self, file, dpi=100, save='png', show=True, size=(7, 7), sep_mod=False)
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File:
-
Only supported 'csv'
-
Start End Type Name Color (Optional) -
Start < End
-
Type: circ, exon, intron, and modifications type
- Modifications type: m6A, m1A, m5C, pU, 2OMe, MRE, RBP, ORF
-
Color: RGB, RGBA, hex, or supported color names.
-
-
Save: file format you wish to save as, PNG, PDF, JPEG, etc.
-
Show: Bool, wheather to show the plot after rendering.
-
Size: (Length, Width) the size of the plot.
-
sep_mod: Bool, prevent the modifications from overlapping if set True.
set_palette
circDraw.set_palette(palette)
A list of colors, the length of the list must bigger than 5.
set_mod_palette
circDraw.set_mod_palette(palette)
A dictionary of colors match with the modification. You can change any one of the modification colors.
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